Variant report

Variant	rs43149
Chromosome Location	chr5:89826193-89826194
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	UBTF	chr5:89824326-89826236	K562	blood:	n/a	n/a
2	GTF2F1	chr5:89825169-89826353	K562	blood:	n/a	n/a
3	CTCF	chr5:89825898-89826198	Medullo	brain:	n/a	n/a
4	TCF12	chr5:89824687-89826218	A549	lung:	n/a	chr5:89825149-89825159
5	RAD21	chr5:89825345-89826271	Hela-S3	cervix:	n/a	chr5:89825493-89825505
6	ZNF143	chr5:89824771-89826429	K562	blood:	n/a	n/a
7	SP1	chr5:89825004-89826212	A549	lung:	n/a	chr5:89825476-89825488 chr5:89825473-89825487 chr5:89825477-89825486 chr5:89825215-89825224 chr5:89825214-89825226 chr5:89825215-89825229 chr5:89825478-89825487 chr5:89825215-89825225 chr5:89825214-89825226 chr5:89825476-89825488 chr5:89825216-89825225
8	POLR2A	chr5:89824308-89826235	K562	blood:	n/a	n/a
9	RAD21	chr5:89825743-89826235	A549	lung:	n/a	n/a
10	IRF1	chr5:89825195-89826614	K562	blood:	n/a	chr5:89826531-89826543 chr5:89826042-89826051
11	CEBPB	chr5:89824300-89826211	Hela-S3	cervix:	n/a	n/a
12	E2F4	chr5:89825944-89826454	MCF10A-Er-Src	breast:	n/a	n/a
13	CTCF	chr5:89825947-89826194	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr5:89824923-89826359	K562	blood:	n/a	n/a
15	ELK1	chr5:89825212-89826215	K562	blood:	n/a	n/a
16	CTCF	chr5:89824880-89826659	SK-N-SH	brain:	n/a	chr5:89825024-89825032
17	RAD21	chr5:89825832-89826270	GM12878	blood:	n/a	n/a
18	IRF1	chr5:89824705-89826239	K562	blood:	n/a	chr5:89824857-89824871 chr5:89826042-89826051
19	CTCF	chr5:89825304-89826369	GM12878	blood:	n/a	n/a
20	NFIC	chr5:89825203-89826206	GM12878	blood:	n/a	n/a
21	RAD21	chr5:89825702-89826329	HepG2	liver:	n/a	n/a
22	POLR2A	chr5:89821851-89826472	K562	blood:	n/a	n/a
23	RFX5	chr5:89824759-89826402	Hela-S3	cervix:	n/a	n/a
24	RAD21	chr5:89825730-89826253	K562	blood:	n/a	n/a
25	EP300	chr5:89824639-89826652	K562	blood:	n/a	chr5:89826147-89826156 chr5:89825539-89825555
26	TRIM28	chr5:89825033-89826579	K562	blood:	n/a	chr5:89826149-89826158
27	MAX	chr5:89824954-89826266	A549	lung:	n/a	chr5:89826147-89826156
28	MAX	chr5:89825932-89826204	H1-hESC	embryonic stem cell:	n/a	chr5:89826147-89826156
29	MAZ	chr5:89824971-89826286	GM12878	blood:	n/a	chr5:89826147-89826156
30	CUX1	chr5:89825849-89826509	K562	blood:	n/a	n/a
31	CTCF	chr5:89825853-89826260	A549	lung:	n/a	n/a
32	PML	chr5:89825539-89826276	K562	blood:	n/a	chr5:89826149-89826158
33	POLR2A	chr5:89825050-89826242	U87	brain:	n/a	n/a
34	ZNF143	chr5:89825174-89826239	GM12878	blood:	n/a	n/a
35	FOS	chr5:89825247-89826371	HUVEC	blood vessel:	n/a	chr5:89826147-89826157 chr5:89826147-89826157 chr5:89826149-89826156 chr5:89826148-89826156 chr5:89826148-89826156 chr5:89826147-89826157
36	SP4	chr5:89825136-89826209	H1-hESC	embryonic stem cell:	n/a	n/a
37	ZC3H11A	chr5:89824872-89826217	K562	blood:	n/a	n/a
38	CTCF	chr5:89825916-89826195	GM12878	blood:	n/a	n/a
39	CTCF	chr5:89825845-89826249	A549	lung:	n/a	n/a
40	RAD21	chr5:89825075-89826375	HCT-116	colon:	n/a	chr5:89825493-89825505
41	ELK1	chr5:89825257-89826203	Hela-S3	cervix:	n/a	n/a
42	RCOR1	chr5:89824569-89826214	Hela-S3	cervix:	n/a	n/a
43	EP300	chr5:89824970-89826268	GM12878	blood:	n/a	chr5:89826147-89826156 chr5:89825539-89825555
44	REST	chr5:89824760-89826356	H1-neurons	neurons:	n/a	chr5:89825143-89825156
45	SP1	chr5:89825047-89826238	A549	lung:	n/a	chr5:89825476-89825488 chr5:89825473-89825487 chr5:89825477-89825486 chr5:89825215-89825224 chr5:89825214-89825226 chr5:89825215-89825229 chr5:89825478-89825487 chr5:89825215-89825225 chr5:89825214-89825226 chr5:89825476-89825488 chr5:89825216-89825225
46	MAFF	chr5:89825803-89826506	K562	blood:	n/a	n/a
47	TEAD4	chr5:89825738-89826305	K562	blood:	n/a	n/a
48	CTCF	chr5:89825926-89826204	Spleen_OC	spleen:	n/a	n/a
49	ZNF384	chr5:89825326-89826377	GM12878	blood:	n/a	n/a
50	RAD21	chr5:89825569-89826287	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:89703358..89707086-chr5:89823955..89827154,6	MCF-7	breast:
2	chr5:89825930..89827528-chr5:89867274..89868949,2	MCF-7	breast:
3	chr5:89716690..89717570-chr5:89825587..89826330,4	MCF-7	breast:
4	chr5:89825899..89828736-chr5:89905925..89909224,3	K562	blood:
5	chr5:89825541..89827508-chr5:89852797..89855537,2	MCF-7	breast:
6	chr5:89708413..89711602-chr5:89825612..89828655,3	K562	blood:
7	chr5:89825681..89827224-chr5:89844315..89846523,2	K562	blood:
8	chr5:89766469..89774126-chr5:89823341..89829105,11	K562	blood:
9	chr5:89822684..89827061-chr5:89851623..89857043,7	MCF-7	breast:
10	chr5:89705290..89707109-chr5:89824364..89826854,3	MCF-7	breast:
11	chr5:89825598..89829055-chr5:89851441..89854747,4	K562	blood:
12	chr5:89704960..89708059-chr5:89823269..89827144,6	K562	blood:
13	chr5:89768855..89773751-chr5:89822671..89829297,12	K562	blood:
14	chr5:89768691..89773005-chr5:89822332..89827140,9	MCF-7	breast:
15	chr5:89703407..89707223-chr5:89822965..89826833,10	K562	blood:
16	chr5:89767818..89772796-chr5:89823286..89827702,11	MCF-7	breast:
17	chr5:89734834..89736191-chr5:89825533..89826967,10	K562	blood:
18	chr5:89825636..89826384-chr5:89900047..89900941,2	K562	blood:

Variant related genes	Relation type
LYSMD3	TF binding region
ENSG00000255647	Chromatin interaction
ENSG00000153140	Chromatin interaction
ENSG00000164199	Chromatin interaction
ENSG00000176055	Chromatin interaction
ENSG00000113356	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10069050	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs154568	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs154569	0.89[EUR][1000 genomes]
rs154570	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs154572	0.84[EUR][1000 genomes]
rs154573	0.85[EUR][1000 genomes]
rs1553545	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs171790	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs250377	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs257850	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs257851	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2656957	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs27201	0.91[EUR][1000 genomes]
rs37238	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs37239	0.83[EUR][1000 genomes]
rs37240	0.83[EUR][1000 genomes]
rs42467	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs491082	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs511393	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs526806	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs556894	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59159252	0.88[ASN][1000 genomes]
rs594990	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs599432	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs679568	0.95[AFR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6884154	0.81[EUR][1000 genomes]
rs810974	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021142	chr5:89102893-89897826	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv537804	chr5:89102893-89897826	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv917025	chr5:89208994-89855436	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv882365	chr5:89770768-89882618	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs43149	LYSMD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89822600-89826600	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr5:89823200-89826200	Active TSS	Right Atrium	heart
3	chr5:89823200-89826200	Active TSS	NHLF	lung
4	chr5:89823400-89826400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr5:89823600-89826200	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr5:89823600-89826200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:89823600-89826200	Active TSS	Fetal Intestine Large	intestine
8	chr5:89823600-89826200	Active TSS	K562	blood
9	chr5:89823600-89826200	Active TSS	NH-A	brain
10	chr5:89823600-89826200	Active TSS	NHDF-Ad	bronchial
11	chr5:89823600-89826400	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr5:89823600-89826400	Active TSS	GM12878-XiMat	blood
13	chr5:89823800-89826200	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr5:89823800-89826200	Active TSS	HMEC	breast
15	chr5:89823800-89826400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr5:89824000-89826200	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr5:89824000-89826200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr5:89824000-89826200	Active TSS	Colonic Mucosa	Colon
19	chr5:89824000-89826200	Active TSS	Colon Smooth Muscle	Colon
20	chr5:89824000-89826200	Active TSS	Right Ventricle	heart
21	chr5:89824000-89826400	Active TSS	H1 Cell Line	embryonic stem cell
22	chr5:89824000-89826400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr5:89824000-89826600	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr5:89824000-89826600	Active TSS	Aorta	Aorta
25	chr5:89824000-89826600	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr5:89824000-89826600	Active TSS	HSMMtube	muscle
27	chr5:89824200-89826200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr5:89824200-89826200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr5:89824200-89826200	Active TSS	Brain Angular Gyrus	brain
30	chr5:89824200-89826200	Active TSS	Brain Anterior Caudate	brain
31	chr5:89824200-89826200	Active TSS	Fetal Intestine Small	intestine
32	chr5:89824200-89826200	Active TSS	Fetal Muscle Trunk	muscle
33	chr5:89824200-89826200	Active TSS	Rectal Mucosa Donor 29	rectum
34	chr5:89824200-89826200	Active TSS	HSMM	muscle
35	chr5:89824200-89826400	Active TSS	Brain Hippocampus Middle	brain
36	chr5:89824200-89826400	Active TSS	Fetal Stomach	stomach
37	chr5:89824200-89826600	Active TSS	Ovary	ovary
38	chr5:89824400-89826200	Active TSS	H9 Cell Line	embryonic stem cell
39	chr5:89824400-89826200	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr5:89824400-89826200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr5:89824400-89826200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr5:89824400-89826200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr5:89824400-89826200	Active TSS	Muscle Satellite Cultured Cells	--
44	chr5:89824400-89826200	Active TSS	Esophagus	oesophagus
45	chr5:89824400-89826200	Active TSS	Left Ventricle	heart
46	chr5:89824400-89826200	Active TSS	Pancreas	Pancrea
47	chr5:89824400-89826200	Active TSS	A549	lung
48	chr5:89824400-89826400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr5:89824400-89826400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr5:89824400-89826400	Active TSS	Psoas Muscle	Psoas

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